mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 14:13:09 +00:00
8d4373b4e8
* added bcftools convert * Update modules/bcftools/convert/main.nf Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> * updated test.yml * Update modules/bcftools/convert/main.nf Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> * added automatic output type detection * linting * removed a trailing whitespace Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
62 lines
2.2 KiB
YAML
62 lines
2.2 KiB
YAML
name: "bcftools_convert"
|
|
description: Converts certain output formats to VCF
|
|
keywords:
|
|
- bcftools
|
|
- convert
|
|
- vcf
|
|
- gvcf
|
|
tools:
|
|
- "bcftools":
|
|
description: "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations."
|
|
homepage: "https://samtools.github.io/bcftools/bcftools.html"
|
|
documentation: "https://samtools.github.io/bcftools/bcftools.html#convert"
|
|
tool_dev_url: "https://github.com/samtools/bcftools"
|
|
doi: "https://doi.org/10.1093/gigascience/giab008"
|
|
licence: "['GPL']"
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- input:
|
|
type: file
|
|
description: |
|
|
The input format. Each format needs a seperate parameter to be specified in the `args`:
|
|
- GEN/SAMPLE file: `--gensample2vcf`
|
|
- gVCF file: `--gvcf2vcf`
|
|
- HAP/SAMPLE file: `--hapsample2vcf`
|
|
- HAP/LEGEND/SAMPLE file: `--haplegendsample2vcf`
|
|
- TSV file: `--tsv2vcf`
|
|
pattern: "*.{gen,sample,g.vcf,hap,legend}{.gz,}"
|
|
- input_index:
|
|
type: file
|
|
description: (Optional) The index for the input files, if needed
|
|
pattern: "*.bed"
|
|
- bed:
|
|
type: file
|
|
description: (Optional) The BED file containing the regions for the VCF file
|
|
pattern: "*.bed"
|
|
- fasta:
|
|
type: file
|
|
description: (Optional) The reference fasta, only needed for gVCF conversion
|
|
pattern: "*.{fa,fasta}"
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
- vcf:
|
|
type: file
|
|
description: The converted VCF file
|
|
pattern: "*.{bam,cram,sam}"
|
|
|
|
authors:
|
|
- "@nvnieuwk"
|